I have cleaned the drain line from the Aframe drain and still I am getting water into my duct work , just had a new motor put in and I was wondering if the drain pan under the
aframe has a seal that could let this water into my duct work.

May be a clogged P-trap on the condensate drip line.
May be a hole in the drip pan under the evaporator coils.
May be the motor is running at too high a speed and blowing the condensate off the evaporator coils and into the ductwork.

Another idea: You may have missing insulation on your cooling line. This COLD line will cause condensation and dripping . . . result is water where you do not want it. Inspect the cooling line carefully.